Yurchenko, A. A., Katolikova, N., Polev, D., Shcherbakova, I. and Strelkov, P. (2018) Transcriptome of the bivalve Limecola balthica L. from Western Pacific: a new resource for studies of European populations. Marine Genomics, 40, pp. 58-63. (doi: 10.1016/j.margen.2018.03.007) (PMID:29657123)
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Abstract
The Baltic clam Limecola balthica L. (Tellinidae) is broadly used in ecophysiological, toxicological, evolutionary and environmental monitoring studies. However, it is poorly studied in respect of genome and gene functions. We obtained a transcriptome of Limecola b. balthica from Kamchatka (Western Pacific) generated with the use of Illumina high-throughput sequencing. We annotated 11,374 proteins, including 53 from the oxidative phosphorylation pathway and a number of pollution-stress biomarkers, recovered 254,540 single nucleotide variants within two annotated transcriptomes including 25,330 scorable in the previously published European data. Our results confirmed the available allozyme data indicating that nuclear genomes of the clams from the Baltic Sea were intermediate in their genetic composition between the Pacific (L. b. balthica) and the Atlantic (L. b. rubra) subspecies. At the same time, the mitochondrial genomes of Limecola from Kamchatka were nearly identical to the single published genome from the Baltic. The genomic diversity in Limecola was found to be high and comparable with that of other marine mollusks (0.0138 and 0.0142 heterozygous positions in the two studied transcriptomes). The data obtained in our study are a valuable resource for further development of genomic markers for evolutionary genetic and ecophysiological studies of L. balthica complex.
| Item Type: | Articles |
|---|---|
| Additional Information: | This work was supported by Russian Foundation for Basic Research, Grant no. 16-04-00723, St. Petersburg State University, Grant no. 0.40.493.2017 and St. Petersburg State University, Grant no. 1.42.967.2016. |
| Keywords: | Assembly, hybridization, Limecola balthica, Macoma balthica, marine biomarkers, transcriptome. |
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Yurchenko, Dr Andrey |
| Authors: | Yurchenko, A. A., Katolikova, N., Polev, D., Shcherbakova, I., and Strelkov, P. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine |
| Journal Name: | Marine Genomics |
| Publisher: | Elsevier |
| ISSN: | 1874-7787 |
| ISSN (Online): | 1876-7478 |
| Published Online: | 12 April 2018 |
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